Title

Author

Date of Award

2017

Degree Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

Graduate Group

Genomics & Computational Biology

First Advisor

Frederic Bushman

Abstract

Microbial involvement in disease has been long-established, but only recently has metagenomics–the study of entire microbial communities–been leveraged in disease research. Powered by advancements in sequencing technologies, metagenomics has been used to better understand a wide variety of diseases, especially in the gastrointestinal tract and other areas with high microbial activity. However, the extreme sensitivity of modern sequencing and lack of established best practices yields high error rates when used in settings with low microbial involvement. To realize the potential of metagenomic sequencing in disease research, we need new high-precision experimental and statistical methods that reach clinical standards of confidence. In this thesis, I describe our search for microbial signatures in sarcoidosis, an idiopathic disease with suspected microbial involvement. Through the use of novel experimental and statistical methods, we were able to eliminate confounding environmental factors and identify the enrichment of Cladosporiaceae fungi in sarcoidosis. I next describe a computational method to recover pathogen genomes from a sample containing mostly host DNA without the use of over-sequencing or culturing. This method enables study of cryptic pathogen genomes and the ability to track genetic variants that may affect virulence or antibiotic resistance. Finally, I demonstrate the integration of metagenomic sequencing with immune repertoire sequencing in patients with severe combined immunodeficiency after gene therapy. This study is the first to describe the changes in an immune-naïve microbiome that occur during the development of a new immune system. We see that the microbiome of these children shift from an abnormal state to one resembling healthy children in conjunction with their restored immunities. These studies lay out methods that improve the precision and utility of metagenomic sequencing for investigating idiopathic and immune disorders.